analyse_variation

Setup Library & Data

library(readr)
library(ggplot2)
library(dplyr)

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

library(gridExtra)

## 
## Attaching package: 'gridExtra'

## The following object is masked from 'package:dplyr':
## 
##     combine

library(tidyr)
library(broom)

ref_values_files <- list.files(path = ".", pattern = "^ref.*\\.csv$", full.names = FALSE)
variation_f_files <- list.files(path = ".", pattern = "^var.*\\.csv$", full.names = FALSE)

ls_ref <- lapply(ref_values_files, function(p){readr::read_csv(p)})

## Rows: 8 Columns: 5
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (3): symbol, units, description
## dbl (2): min, max
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 8 Columns: 5
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (3): symbol, units, description
## dbl (2): min, max
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 10 Columns: 5
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (3): symbol, units, description
## dbl (2): min, max
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 8 Columns: 5
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (3): symbol, units, description
## dbl (2): min, max
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 10 Columns: 5
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (3): symbol, units, description
## dbl (2): min, max
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 12 Columns: 5
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (3): symbol, units, description
## dbl (2): min, max
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 9 Columns: 5
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (3): symbol, units, description
## dbl (2): min, max
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 10 Columns: 5
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (3): symbol, units, description
## dbl (2): min, max
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 8 Columns: 5
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (3): symbol, units, description
## dbl (2): min, max
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

names(ls_ref) <- lapply(ref_values_files, function(n){sub(".* - (.*?)\\..*", "\\1", n)})

ls_var <- lapply(variation_f_files, function(p){
  readr::read_csv(p, col_types = cols(prd = col_double(), data = col_double()))
})
names(ls_var) <- lapply(variation_f_files, function(n){sub(".* - (.*?)\\..*", "\\1", n)})

names(ls_var) == names(ls_ref)

## [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE

Perdix perdix

name = "Perdix_perdix"
unique(ls_var[[name]]$description)

##  [1] "age at birth"                          
##  [2] "time since birth at fledging"          
##  [3] "time since birth at puberty"           
##  [4] "time since birth at first reproduction"
##  [5] "life span"                             
##  [6] "initial wet weight"                    
##  [7] "wet weight at birth"                   
##  [8] "ultimate wet weight"                   
##  [9] "ultimate wet weight for males"         
## [10] "maximum reprod rate"

unique(ls_var[[name]]$symbol)

##  [1] "ab"   "tx"   "tp"   "tR"   "am"   "Ww0"  "Wwb"  "Wwi"  "Wwim" "Ri"

varNames = list(
'1'="age at birth, ab",
'2'="time since birth at fledging, tx",
'3'="time since birth at puberty, tp",
'4'="time since birth at first reproduction, tR",
'5'="life span, am",
'6'="initial wet weight, Ww0",
'7'="wet weight at birth, Wwb",
'8'="ultimate wet weight, Wwi",
'9'="ultimate wet weight for males, Wwim",
'10'="maximum reprod rate, Ri" 
)

ls_p = plts(name, varNames)

## Joining with `by = join_by(symbol, units, description)`

ls_p[[1]]

## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning
## -Inf

# gridExtra::grid.arrange(g1,g2)

ls_p[[2]]

Motacilla_flava

name = "Motacilla_flava"
unique(ls_var[[name]]$description)

## [1] "age at birth"                  "time since birth at fledging" 
## [3] "time since birth at puberty"   "time since birth at 1st brood"
## [5] "life span"                     "wet weight at birth"          
## [7] "ultimate wet weight"           "maximum reprod rate"

unique(ls_var[[name]]$symbol)

## [1] "ab"  "tx"  "tp"  "tR"  "am"  "Wwb" "Wwi" "Ri"

varNames = list(
'1'="age at birth, ab",
'2'="time since birth at fledging, tx",
'3'="time since birth at puberty, tp",
'4'="time since birth at 1st brood, tR",
'5'="life span, am",
'6'="wet weight at birth, Wwb",
'7'="ultimate wet weight, Wwi",
'8'="maximum reprod rate, Ri" 
)

ls_p = plts(name, varNames)

## Joining with `by = join_by(symbol, units, description)`

ls_p[[1]]

## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning
## -Inf
## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning
## -Inf

# gridExtra::grid.arrange(g1,g2)

ls_p[[2]]

Alauda arvensis

name = "Alauda_arvensis"
unique(ls_var[[name]]$description)

## [1] "age at birth"                  "time since birth at fledging" 
## [3] "time since birth at puberty"   "time since birth at 1st brood"
## [5] "life span"                     "wet weight at birth"          
## [7] "ultimate wet weight"           "maximum reprod rate"

unique(ls_var[[name]]$symbol)

## [1] "ab"  "tx"  "tp"  "tR"  "am"  "Wwb" "Wwi" "Ri"

varNames = list(
'1'="age at birth, ab",
'2'="time since birth at fledging, tx",
'3'="time since birth at puberty, tp",
'4'="time since birth at 1st brood, tR",
'5'="life span, am",
'6'="wet weight at birth, Wwb",
'7'="ultimate wet weight, Wwi",
'8'="maximum reprod rate, Ri" 
)

ls_p = plts(name, varNames)

## Joining with `by = join_by(symbol, units, description)`

ls_p[[1]]

## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning
## -Inf

# gridExtra::grid.arrange(g1,g2)

ls_p[[2]]

Turdus_philomelos

name = "Turdus_philomelos"
unique(ls_var[[name]]$description)

## [1] "age at birth"                   "time since birth at fledging"  
## [3] "time since birth at puberty"    "time since birth at 1st brood" 
## [5] "life span"                      "wet weight at birth"           
## [7] "ultimate wet weight for female" "maximum reprod rate"

unique(ls_var[[name]]$symbol)

## [1] "ab"  "tx"  "tp"  "tR"  "am"  "Wwb" "Wwi" "Ri"

varNames = list(
'1'="age at birth, ab",
'2'="time since birth at fledging, tx",
'3'="time since birth at puberty, tp",
'4'="time since birth at 1st brood, tR",
'5'="life span, am",
'6'="wet weight at birth, Wwb",
'7'="ultimate wet weight, Wwi",
'8'="maximum reprod rate, Ri" 
)

ls_p = plts(name, varNames)

## Joining with `by = join_by(symbol, units, description)`

ls_p[[1]]

## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning
## -Inf

# gridExtra::grid.arrange(g1,g2)

ls_p[[2]]

Sorex_araneus

name = "Sorex_araneus"
unique(ls_var[[name]]$description)

##  [1] "gestation time"              "time since birth at weaning"
##  [3] "time since birth at puberty" "life span"                  
##  [5] "ultimate total length"       "wet weight at birth"        
##  [7] "wet weight at weaning"       "wet weight at puberty"      
##  [9] "ultimate wet weight"         "maximum reprod rate"

unique(ls_var[[name]]$symbol)

##  [1] "tg"  "tx"  "tp"  "am"  "Li"  "Wwb" "Wwx" "Wwp" "Wwi" "Ri"

varNames = list(
'1'="gestation time, tg",
'2'="time since birth at weaning, tx",
'3'="time since birth at puberty, tp",
'5'="life span, am",
'6'="ultimate total length, Li",
'7'="wet weight at birth, Wwb",
'8'="wet weight at weaning, Wwx",
'9'="wet weight at puberty, Wwp",
'10'="ultimate wet weight, Wwi",
'11'="maximum reprod rate, Ri" 
)

ls_p = plts(name, varNames)

## Joining with `by = join_by(symbol, units, description)`

ls_p[[1]]

## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning
## -Inf
## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning
## -Inf
## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning
## -Inf

# gridExtra::grid.arrange(g1,g2)

ls_p[[2]]

Crocidura_russula

name = "Crocidura_russula"
unique(ls_var[[name]]$description)

## [1] "gestation time"              "time since birth at weaning"
## [3] "time since birth at puberty" "life span"                  
## [5] "wet weight at birth"         "wet weight at weaning"      
## [7] "ultimate wet weight"         "maximum reprod rate"

unique(ls_var[[name]]$symbol)

## [1] "tg"  "tx"  "tp"  "am"  "Wwb" "Wwx" "Wwi" "Ri"

varNames = list(
'1'="gestation time, tg",
'2'="time since birth at weaning, tx",
'3'="time since birth at puberty, tp",
'5'="life span, am",
'6'="wet weight at birth, Wwb",
'7'="wet weight at weaning, Wwx",
'8'="ultimate wet weight, Wwi",
'9'="maximum reprod rate, Ri" 
)

ls_p = plts(name, varNames)

## Joining with `by = join_by(symbol, units, description)`

ls_p[[1]]

# gridExtra::grid.arrange(g1,g2)

ls_p[[2]]

Ichthyosaura_alpestris

name = "Ichthyosaura_alpestris"
unique(ls_var[[name]]$description)

##  [1] "life span"                       "SVL at metam for females"       
##  [3] "SVL at puberty for females"      "SVL at puberty for males"       
##  [5] "ultimate SVL for females"        "ultimate SVL for males"         
##  [7] "wet weight at birth"             "ultimate wet weight for females"
##  [9] "ultimate wet weight for males"   "maximum reprod rate"

unique(ls_var[[name]]$symbol)

##  [1] "am"   "Lj"   "Lp"   "Lpm"  "Li"   "Lim"  "Wwb"  "Wwi"  "Wwim" "Ri"

varNames = list(
'1'="life span, am",
'2'="SVL at metam for females, Lj",
'3'="SVL at puberty for females, Lp",
'4'="SVL at puberty for males, Lpm",
'5'="ultimate SVL for females, Li",
'6'="ultimate SVL for males, Lim",
'7'="wet weight at birth, Wwb",
'8'="ultimate wet weight for females, Wwi",
'9'="ultimate wet weight for males, Wwim",
'10'="maximum reprod rate, Ri" 
)

ls_p = plts(name, varNames)

## Joining with `by = join_by(symbol, units, description)`

ls_p[[1]]

## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning
## -Inf
## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning
## -Inf
## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning
## -Inf
## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning
## -Inf

## Warning: Removed 2 rows containing missing values or values outside the scale range
## (`geom_point()`).

# gridExtra::grid.arrange(g1,g2)

ls_p[[2]]

## Warning: Removed 2 rows containing non-finite outside the scale range (`stat_smooth()`).
## Removed 2 rows containing non-finite outside the scale range (`stat_smooth()`).

## Warning: Removed 2 rows containing missing values or values outside the scale range
## (`geom_point()`).

Rana_temporaria

name = "Rana_temporaria"
unique(ls_var[[name]]$description)

## [1] "age at birth"                "time since birth at metam"  
## [3] "time since metam at puberty" "life span"                  
## [5] "body length at metam"        "ultimate body length"       
## [7] "wet weight at birth"         "ultimate wet weight"        
## [9] "maximum reprod rate"

unique(ls_var[[name]]$symbol)

## [1] "ab"  "tj"  "tp"  "am"  "Lj"  "Li"  "Wwb" "Wwi" "Ri"

varNames = list(
'1'="age at birth, ab",
'2'="time since birth at metam, tj",
'3'="time since metam at puberty, tp",
'4'="life span, am",
'5'="body length at metam, Lj",
'6'="ultimate body length, Li",
'7'="wet weight at birth, Wwb",
'8'="ultimate wet weight, Wwi",
'9'="maximum reprod rate, Ri" 
)

ls_p = plts(name, varNames)

## Joining with `by = join_by(symbol, units, description)`

ls_p[[1]]

## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning
## -Inf
## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning
## -Inf
## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning
## -Inf

# gridExtra::grid.arrange(g1,g2)

ls_p[[2]]

Podarcis_muralis

name = "Podarcis_muralis"
unique(ls_var[[name]]$description)

##  [1] "time since birth at puberty"   "life span"                    
##  [3] "SVL at hatching"               "SVL at puberty for females"   
##  [5] "SVL at puberty for males"      "ultimate SVL for females"     
##  [7] "ultimate SVL for males"        "wet weight of eggs"           
##  [9] "wet weight of hatchlings"      "ultimate wet weight"          
## [11] "ultimate wet weight for males" "maximum reprod rate"

unique(ls_var[[name]]$symbol)

##  [1] "tp"   "am"   "Lb"   "Lp"   "Lpm"  "Li"   "Lim"  "Ww0"  "Wwb"  "Wwi" 
## [11] "Wwim" "Ri"

varNames = list(
'1'="time since birth at puberty, tp",
'2'="life span, am",
'3'="SVL at hatching, Lb",
'4'="SVL at puberty for females, Lp",
'5'="SVL at puberty for males, Lpm",
'6'="ultimate SVL for females, Li",
'7'="ultimate SVL for males, Lim",
'8'="wet weight of eggs, Ww0", 
'9'="wet weight of hatchlings, Wwb",
'10'="ultimate wet weight, Wwi",
'11'="ultimate wet weight for males, Wwim",
'12'="maximum reprod rate, Ri" 
)

ls_p = plts(name, varNames)

## Joining with `by = join_by(symbol, units, description)`

ls_p[[1]]

## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning
## -Inf
## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning
## -Inf
## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning
## -Inf
## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning
## -Inf
## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning
## -Inf

# gridExtra::grid.arrange(g1,g2)

ls_p[[2]]